Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,544,9260TA54.5% 1.2 / 12.9 11N178K (AAT→AAA) uxuRUxu operon transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base A (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCAGTTCCATCTCGCTATTGCCGAAGCAACGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTGGATGACAGCCTGTATCGCAAAGAGTGGTTGGGC  >  NZ_CP009273/4544837‑4544989
                                                                                         |                                                               
aTGCAGTTCCATCTCGCTATTGCCGAAGCAACGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAAt                                                                 <  1:91610/90‑1 (MQ=255)
     gTTCCATCTCGCTATTGCCGAAGCAACGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGGAAAAAAACCaaa                                                            >  2:329567/1‑89 (MQ=255)
                          aGCAACGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCa                                       <  1:126044/90‑1 (MQ=255)
                              aCGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTg                                   <  1:320841/90‑1 (MQ=255)
                                        gCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGGAAAAAAACCAAAGTGGGTCCCGTTGCACAGCCATCTGGGTGACAGcc                         >  1:147830/1‑90 (MQ=255)
                                        gCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAAACCAATGTGGGTCCAATTGCACAGCCATCTGGATGACAggc                         >  2:180441/1‑88 (MQ=255)
                                        gCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAAAAAACCAAAGTGGGTCCCGGTGCCCAGCCACCTTGTTGACAccc                         >  2:256775/1‑90 (MQ=255)
                                          aTGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTGGATGACAGCCTg                       <  2:147830/90‑1 (MQ=255)
                                           tGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAAAAAACCAAAGTGGGTCCCGTTGCACAGCCCCCTGGGTGACAGCCCGt                      >  1:80808/1‑90 (MQ=255)
                                               ggtggAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAAAAAACCAAAGTGGGTCCCGTTGCACACCCCCCTGGGGGAAAGCCCGTATCg                  >  1:8991/1‑90 (MQ=255)
                                                           ccGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTGGATGACAGCCTGTATCGCAAAGAGTGGtt      <  1:13510/90‑1 (MQ=255)
                                                               cAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTGGATGACAGCCTGTATCGCAAAGAGTGGTTGGGc  <  1:256775/90‑1 (MQ=255)
                                                                                         |                                                               
ATGCAGTTCCATCTCGCTATTGCCGAAGCAACGCATAACAGCATGCTGGTGGAGCTGTTCCGTCAGTCCTGGCAGTGGCGGGAAAACAATCCAATGTGGATCCAGTTGCACAGCCATCTGGATGACAGCCTGTATCGCAAAGAGTGGTTGGGC  >  NZ_CP009273/4544837‑4544989

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑